arXiv:2603.12307q-bio.QMeess.IV2026-03

无需初始参数,直接从二维图像重建螺旋分子三维结构

SHREC: A Spectral Embedding-Based Approach for Ab-Initio Reconstruction of Helical Molecules

  • 利用谱嵌入方法提取螺旋片段投影的低维流形结构
  • 在公开数据集上实现高分辨率重建,准确恢复螺旋参数
  • 适合无先验知识的螺旋分子自动重构,提升可靠性

冷冻电镜(cryo-EM)已成为在近原子分辨率下解析生物大分子三维结构的强大工具。然而,螺旋组装体的重构面临独特挑战,因其固有的对称性及未知螺旋对称参数的需求。传统方法需准确估计这些参数,通常依赖试错或先验知识,易导致错误重构,限制了从头重建的可靠性。本文提出SHREC(Spectral Helical REConstruction)算法,可直接从二维cryo-EM图像中恢复螺旋片段的投影角度,无需事先知晓螺旋对称参数。该方法基于投影形成一维流形的洞察,采用谱嵌入技术进行恢复。在公开数据集上的实验验证表明,SHREC在仅需已知轴向对称群的前提下,实现了高分辨率重建并准确恢复螺旋参数。通过消除对初始对称性估计的需求,SHREC为cryo-EM中螺旋结构的重建提供了一条更鲁棒、自动化的路径。

原文摘要 · Abstract (English)

Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for determining the three-dimensional structures of biological molecules at near-atomic resolution. However, reconstructing helical assemblies presents unique challenges due to their inherent symmetry and the need to determine unknown helical symmetry parameters. Traditional approaches require an accurate initial estimation of these parameters, which is often obtained through trial and error or prior knowledge. These requirements can lead to incorrect reconstructions, limiting the reliability of ab initio helical reconstruction. In this work, we present SHREC (Spectral Helical REConstruction), an algorithm that directly recovers the projection angles of helical segments from their two-dimensional cryo-EM images, without requiring prior knowledge of helical symmetry parameters. Our approach leverages the insight that projections of helical segments form a one-dimensional manifold, which can be recovered using spectral embedding techniques. Experimental validation on publicly available datasets demonstrates that SHREC achieves high resolution reconstructions while accurately recovering helical parameters, requiring only knowledge of the specimen's axial symmetry group. By eliminating the need for initial symmetry estimates, SHREC offers a more robust and automated pathway for determining helical structures in cryo-EM.

冷冻电镜螺旋重构谱嵌入结构生物学

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